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The following is kept as an archive, but probably won't be updated regularly.

Welcome to the Indiana Cheminformatics Education Portal (ICEP). is a repository of freely accessible cheminformatics educational materials maintained by David Wild, director of the Indiana University Cheminformatics Program. The purpose of this repository is to broaden education in cheminformatics, an effort that includes several other initiatives including an innovative cheminformatics distance education program, a Graduate Certificate in Chemical Informatics from Indiana University, a low cost cheminformatics self-study guide, and a collaboration with Open Source Drug Discovery for sharing of cheminformatics educational materials. ICEP includes free introductory learning materials, videos, and news, social media, and latest journal articles relating to cheminformatics.


New!!

We now are running a free online introductory cheminformatics course - it's not too late to join.

ICEP's wiki-based introductory cheminformatics learning materials


The following introductory topics are adapted from materials that we use in our I571 Chemical Information Technology class, which serves as our introductory cheminformatics course at Indiana University. These themes are developed further in the Introducing Cheminformatics eBook


Free short tutorial videos





Introducing Cheminformatics eBook now available for $25 - also available in library and company versions



external image icbookcover.jpg?height=200&width=154New eBook! - Introducing Cheminformatics: an intensive self-study guide.
This Lulu PDF eBook gives an intensive introduction to cheminformatics, including the history of the field, representing 2D and 3D chemical structures on computer, storing and using databases of chemical and related biological information, handling chemical information on the web and in the scholarly literature, and giving an overview of some advanced topics such as clustering and diversity, QSAR and predictive modeling, 3D alignment and docking, and software toolkits cheminformatics software. It is aimed at life scientists and computer scientists in both industry and academia who need a rapid, flexible introduction to this field, and comes as a regular PDF. It is available in an individual version for $25, or in versions that can be used in an academic library system or company-wide. For more information, check out the eBook on Lulu.


Other learning resources




Cheminformatics news, blogs and social media




    So much to do, so little time
    • Waterfall Plots for Dose Response Curves by Rajarshi Guha Sep 20, 2017
      Waterfall plots are a common visualization method to view multiple spectra and have some similarities with joy plots. In the high throughput screening world, people have plot multiple dose response curves, offset on the z-axis to produce something...
    • Survey Software Developer Opportunity by Rajarshi Guha Mar 8, 2017
      On behalf of Prof. Debarchana Ghosh (UConn): I’m designing a survey to collect information about a person’s daily activities in their neighborhood and their social networks, i.e. the people they meet and talk to. Examples of daily...
    • CSA Trust Grant – Call for Proposals by Rajarshi Guha Feb 20, 2017
      Applications Invited for CSA Trust Grant for 2017 The Chemical Structure Association (CSA) Trust is an internationally recognized organization established to promote the critical importance of chemical information to advances in chemical research....
    • Endnote XML to HTML or LaTeX by Rajarshi Guha Dec 31, 2016
      Over the last few years I’ve been maintaining my publication list as a BibTeX file, managed by BibDesk. This is handy when writing papers, but it’s also useful to use this data to keep my CV updated or generate a publications...
    • Freedom from the IF: Impact Neutral Publishing by Rajarshi Guha Dec 26, 2016
      I came across a post from Jan Jensen a few months ago about a GRC meeting that he had attended. What caught my eye however, was his comment on “impact neutral” publishing. Specifically, he mentions For me “impact neutrality&rdquo...
    • Deep Learning in Chemistry by Rajarshi Guha Nov 8, 2016
      Deep learning (DL) is all the rage these days and this approach to predictive modeling is being applied to a wide variety of problems, including many in computational drug discovery. As a dilettante in the area of deep learning, I’ve been fo...
    • A Report from a Stranger in a Strange Land by Rajarshi Guha Oct 26, 2016
      I just got back from ACoP7, the yearly meeting of the International Society of Pharmacometrics (ISoP). Now, I don’t do any PK/PD modeling (hence the “strange land”) but was invited to talk about our high throughput screening plat...
    • From Algorithmic Fairness to QSAR Models by Rajarshi Guha Aug 8, 2016
      The topic of algorithmic fairness has started recieving a lot of attention due to the ability of predictive models to make decisions that might discriminate against certain classes of people. The reasons for this include biased training data, corr...
    • Database Licensing & Sustainability by Rajarshi Guha May 14, 2016
      Update (07/28/16): DrugBank/OMx have updated the licensing conditions for DrugBank data in response to concerns raised earlier by various people and groups. See here for a detailed response from Craig Knox A few days back I came across, via my Twi...
    • SLAS 2017: Let There Be Light: Informatics Approaches to Exploring the Dark Genome by Rajarshi Guha May 11, 2016
      I’m organizing a symposium at the 2017 SLAS meeting in Washington D.C in the Data Analysis and Informatics track. The topic of the symposium focuses on informatics approaches that shed light and explore the dark genome. The description is gi...

    chem-bla-ics
    • New paper: "RDFIO: extending Semantic MediaWiki for interoperable biomedical data management" by Egon Willighagen Sep 9, 2017
      Figure 10 from the article showing what the DrugMet wikiwith the pKa data looked like. CC-BY.When I was still doing research at Uppsala University, I had a internship student, Samuel Lampa, who did wonderful work on knowledge representation and lo...
    • DataCite: the PubMed for data and software by Egon Willighagen Aug 27, 2017
      We have services like PubMed, Europe PMC, and Google Scholar to make a list of literature. Scholia/Wikidata and ORCID are upcoming services, but for data and software there are fewer options. One notable exception is DataCite (two past blogs ...
    • Updated HMDB identifier scheme by Egon Willighagen Aug 26, 2017
      I have not found further details about it yet, but noticed half an hour ago that the Human Metabolome Database (doi:10.1093/nar/gks1065) seems to have changes all their identifiers: the added extra zeros. The screenshot for D-fructose on the ...
    • What about postprint servers? by Egon Willighagen Aug 26, 2017
      Various article version types, including pre and post.Source: SHERPA/ROMEO.Now that preprint servers are picking up speed, let's talk about postprint servers. Sure, we have plenty of places to place and find discussions about the content of articl...
    • Text mining literature that mention JRC representative nanomaterials by Egon Willighagen Aug 17, 2017
      The week before a short holiday in France (nature, cycling, hiking, touristic CERN visit; thanks to Philippe for the ViaRhone tip!), I did some further work on contentmining literature that mention the JRC representative nanomaterials. One im...
    • Wikidata visualizes SMILES strings with John Mayfield's CDK Depict by Egon Willighagen Jul 30, 2017
      SVG depiction of D-ribulose.Wikidata is building up a curated collection of information about chemicals. A lot of data originates from Wikipedia, but active users are augmenting this information. Of particular interest, in this respect, is Se...
    • new paper: "A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury" by Egon Willighagen Jul 5, 2017
      Figure from the article. CC-BY.One of the projects I worked on at Karolinska Institutet with Prof. Grafström was the idea of combining transcriptomics data with dose-response data. Because we wanted to know if there was a relation betwee...
    • The Elsevier-SciHub story by Egon Willighagen Jun 24, 2017
      I blogged earlier today why I try to publish all my work gold Open Access. My ImpactStory profile shows I score 93% and note that with that 10% of the scientists in general score in that range. But then again, some publisher do make it hard for us...
    • As a PhD student, I was often confronted with Closed Access. by Egon Willighagen Jun 24, 2017
      It sounds like a problem not so common in western Europe, but it was when I was a fresh student (around 1994). The Radboud's University Library certainly did not have all journals and for one journal I had to go to a research department and s...
    • You are what you do, or how people got to see me as an engineer by Egon Willighagen Jun 11, 2017
      Source, Wikicommons, CC-BY-SA.Over the past 20 years I have had endless discussions into what the research is that I do. Many see my work as engineer, but I vigorously disagree. But some days it's just too easy to give up and explain things y...

    Useful Chemistry
    • Matthew McBride wins Nov 2012 ONS Challenge Award by Jean-Claude Bradley Nov 16, 2012
      Matthew McBride, an undergraduate chemistry major at Drexel University working in the Bradley Laboratory, was awarded the November 2012 Open Notebook Science Challenge Award sponsored by the Royal Society of Chemistry.  ChemSpider founder Ant...
    • MiniSymposium Bradley Lab 2011 by Jean-Claude Bradley Oct 5, 2011
      I recently presented a 15 minute summary of the current research in my lab on September 29, 2011 at the Drexel University Department of Chemistry Faculty Mini-Symposium. The main project discussed was the Open Melting Point Collection done in coll...
    • Patrick Ndungu talk at Drexel on Nanotechnology by Jean-Claude Bradley Aug 18, 2011
      One of my former Ph. D. students, Patrick Ndungu (now at University of KwaZulu Natal, South Africa) will be speaking at Drexel University on Friday August 19, 2011 at 12:30 in Disque 109. Some Interesting Perspectives on the Integration of Nanoma...
    • Google Apps Scripts Workshop at Drexel University by Jean-Claude Bradley Aug 17, 2011
      Andrew Lang will be in Philadelphia next week and we will be running a workshop on Leveraging Google Spreadsheets with Scripts for Research and Teaching. Now that our institution is no longer providing Microsoft Office for students in the fall te...
    • Open Melting Point Collection Book Edition 1 by Jean-Claude Bradley Aug 11, 2011
      Several months of work through a collaboration between myself, Andrew Lang, Antony Williams and Evan Curtin have culminated in the publication of an Open Melting Point Collection Book. Like our other books on solubility and Reaction Attempts, the...
    • Rapid analysis of melting point trends and models using Google Apps Scripts by Jean-Claude Bradley Jul 19, 2011
      I recently reported on how Google Apps Scripts can be used to facilitate the recording and calculations associated with a chemistry laboratory notebook. (also see resource page)I will demonstrate here how these scripts can be used to rapidly disco...
    • Practical Tips on using Google Apps Scripts for Chemistry Applications by Jean-Claude Bradley Jul 14, 2011
      A few weeks ago I described our use of Google Apps Scripts, developed by Rich Apodaca and Andrew Lang, as an intuitive interface to information related to a chemistry laboratory notebook. Since then we have been using these tools to actively plan...
    • Open Notebook Science Talk at HUBbub 2011 by Jean-Claude Bradley Jul 1, 2011
      On April 6, 2011 I presented at the HUBzero Conference in Indianapolis on "Open Notebook Science: Does Transparency Work?".This presentation will first describe Open Notebook Science, the practice of making the laboratory notebook and all associat...
    • The 4-benzyltoluene melting point twist by Jean-Claude Bradley Jun 22, 2011
      Evan Curtin and I were in the lab this morning to follow up on our effort to curate the melting point of 4-benzyltoluene. I identified the next step to confirm an upper limit of -15 C:With the information available thus far from our experiments (...
    • Google Apps Scripts for an intuitive interface to organic chemistry Open Notebooks by Jean-Claude Bradley Jun 18, 2011
      Rich Apodaca recently demonstrated how Google Apps Scripts can be added to Google Spreadsheets to enable simple calling of web services for chemistry applications (gChem). Although we have been using web service calls from within a Google spreads...

    Noel O'Blog
    • How many cheminformaticians does it take to read a SMILES string? by Noel O'Boyle Yesterday
      A few days ago I posted the following poll question on Twitter:How many Hs are on the N in the molecule described by this SMILES string? N(C)(C)(C)CI provided four possible answers:ZeroOneDependsCan't say as no such moleculePlease take a moment to...
    • My ACS talk on Kekulization and aromatic SMILES by Noel O'Boyle Aug 28, 2017
      Here are the slides for the talk I presented last week at the ACS meeting in Washington. It describes my understanding of the Daylight toolkit as deduced by John: We need to talk about Kekulization, Aromaticity and SMILES from baoilleach The fu...
    • Faster toolkit, faster! by Noel O'Boyle Jul 23, 2017
      After an extended hiatus, I've been back doing a bit of work on Open Babel, and specifically I've been working on improving performance. Basic reading and writing of molecules should be limited by disk I/O speed and not CPU, but this is not (yet) ...
    • Using WebLogo3 to create a sequence logo from Python by Noel O'Boyle May 5, 2017
      A sequence logo is a way to display the variation at particular positions of multiple-aligned sequences. Here I used WebLogo 3 to do this. The documentation is not great, even once you find it, and working out how to do my specific use case requir...
    • Whiskas statistics and the pitfalls of mean rank by Noel O'Boyle Jan 23, 2017
      In the fingerprint similarity paper I published last year, I made the following observation: "However the use of the mean rank is itself problematic as the pairwise similarity of two methods can be altered (and even inverted) by adding additional ...
    • Counting hydrogens in a SMILES string - The Rules by Noel O'Boyle Jan 14, 2017
      Hydrogens are not usually listed explicitly in a SMILES string, but instead can be inferred from a set of rules. To be precise, when reading a SMILES, the position of every hydrogen is known unambiguously once you know the rules. Oh - did I forget...
    • The clockwisdom of SMARTS by Noel O'Boyle Dec 30, 2016
      In earlier posts I discussed/investigated how stereochemistry is represented in SMILES. Here I'm going to try to figure out what I thought would be relatively simple, how to write a SMARTS pattern that matches a chiral molecule and all of its supe...
    • Open Babel 2.4.0 released by Noel O'Boyle Sep 23, 2016
      As announced by Geoff on the mailing list, Open Babel 2.4.0 is now available to download:I'm pleased to announce that Open Babel 2.4.0 has finally been released.This release represents a major update and should be a stable upgrade, strongly recomm...
    • My new thing - providing manuscript images as PDFs by Noel O'Boyle Aug 21, 2016
      My latest oeuvre (on the topic of which fingerprint is best) was published by J. Cheminf. a few weeks ago. For the first time, instead of providing the images as PNGs, I submitted them as PDFs.You see, John had worked me over. At the start, I thou...
    • Open Source Cheminformatics Toolkits - they keep on coming by Noel O'Boyle Aug 2, 2016
      It has been just over three years since I last surveyed the world of open source cheminformatics toolkits. So what's new?Kekule.js - This is a JavaScript toolkit by Chen Jiang with an associated publication in JCIM this year. JavaScript cheminform...

    petermr's blog
    • WLIC/IFLA2017: UBER for scholarly communications and libraries? It’s already here… by pm286 Aug 21, 2017
      WLIC/IFLA2017: UBER for scholarly communications and libraries? It’s already here… You all know of the digital revolution that is changing the world of service - Amazon, UBER, AirBnB, coupled to Facebook, Google, Siri, etc. The common...
    • ContentMine at IFLA2017: The future of Libraries and Scholarly Communications by pm286 Aug 21, 2017
      ContentMine at IFLA2017: The future of Libraries and Scholarly Communications   I am delighted to have been invited to talk at IFLA (https://www.ifla.org/annual-conference), the global overarching body for Libraries of all sorts. I’m in...
    • What is TextAndData/ContentMining? by pm286 Jul 11, 2017
      What is TextAndData/ContentMining? I prefer “ContentMining” to the formal legal phrase “Text and Data Mining” because it emphasizes all kinds of content - audio, photos, videos, diagrams, chemistry, etc. I chose it to asser...
    • Text and Data Mining: Overview by pm286 Jul 11, 2017
      Text and Data Mining: Overview Tomorrow The University of Cambridge Office of Scholarly Communication is running a 1-day Symposium on Text and Data Mining (https://docs.google.com/document/d/1l4N2fSFgpL3iMbjKC3IxHz7GpNVvERB5NzxqWp8jZQo/edit ). I h...
    • How Wikidata can change the world of scientific information 1/n by pm286 Nov 5, 2016
      We're getting involved in Wikidata! It will change the world of scientific (and other) information. So here is an emerging conversation, hopefully over several blog posts. Wicki: Hang on! What's Wikidata? And Wikimedia? I've heard of Wikipedia, bu...
    • The critical role of e-Theses: award acceptance speech at NDLTD by pm286 Jul 12, 2016
      I am honoured by this award; I ‘ll describe the current struggle for ownership of digital scholarly knowledge, emphasize young people and machine-understandable theses and suggest practices.   Early Career Researchers see the digital li...
    • "Dialogue" with Elsevier - story-2 ("Despicable" Legal Weasel Words) by pm286 May 26, 2016
      ContentMine is going to mine the whole scholarly literature (10,000 articles every day). We'd hoped to do this some months ago and one of the reasons is the massive pushback from major publishers. Technically, legally , politically. UK government ...
    • "Dialogue" with Elsevier - story-1 (Will Elsevier publish Crystallographic Data?) by pm286 May 24, 2016
      TL;DR. I continue to try to get public data out of Elsevier. I think I should be able to - every other publisher has no problem. After some not-very-useful replies Elsevier simply give up answering me. Over the last 7-8 … Continue reading &...
    • Taxi Ken and I discuss the UK's negotiations with Elsevier by pm286 May 23, 2016
      When I go the airport by taxi [1] I try to get the same taxi driver, Ken [2]. Ken is a shining example of why every citizen of the world needs access to the whole scholarly literature - open and … Continue reading →
    • Sci-Hub and my personal position on legality 5/n by pm286 May 6, 2016
      I have just blogged on the legal aspects of ContentMining: https://blogs.ch.cam.ac.uk/pmr/2016/05/06/sci-hub-and-legal-aspects-of-contentmining/ (which also contains links to previous blogs. These are general considerations but also relevant to th...



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